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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...and accurate s. Additionally, the underrepresented Y-linked exons provide a valuable benchmark for refining those sequencing technologies while improving the assembly of the highly heterochromatic and often neglected Drosophila Y Chromosome.Long-read sequencing (LRS) technologies Pacific Biosciences (Pac...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...between TEs and satDNAs have been observed for some time, and there is growing evidence that TEs are a prolific source of satellite sequences (for review, see Zattera and Bruschi 2022). High-quality assemblies of three Drosophila virilis group species showed that much of the divergence in composition...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...-specific expression patterns in P. picta and P. parae strongly suggest the convergent evolution of a “Drosophila-like” dosage compensation mechanism through a male-specific hyperexpression of the X Chromosome (Conrad and Akhtar 2012; Darolti et al. 2019; Metzger et al. 2021). Third, our study suggests convergent...
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Research: The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease
- Laure K. Case,
- Emma H. Wall,
- Julie A. Dragon,
- Naresha Saligrama,
- Dimitry N. Krementsov,
- Mohamad Moussawi,
- James F. Zachary,
- Sally A. Huber,
- Elizabeth P. Blankenhorn,
- and Cory Teuscher
Genome Res. September 2013 23: 1474-1485; Published in Advance June 25, 2013, doi:10.1101/gr.156703.113
..., as in Drosophila , these data establish the mammalian ChrY as a member of the regulatory genome due to its ability to epigenetically regulate genome-wide gene expression in immune cells. Footnotes ↵ 6 Corresponding author E-mail C.Teuscher@uvm.edu [Supplemental material is available...
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Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
...) reveals extensive shuffling between species, but most of the orthologous blocks are located in the same Muller elements, suggesting that even on a small scale, translocations rarely occur between chromosomes in the course of Drosophila evolution, consistent with previous observations (Muller 1940...
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Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
- Sahin Naqvi,
- Daniel W. Bellott,
- Kathy S. Lin,
- and David C. Page
Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
.... PLoS Biol 10: e1001328. ↵Kaiser VB, Zhou Q, Bachtrog D. 2011. Nonrandom gene loss from the Drosophila miranda neo-Y chromosome. Genome Biol Evol 3: 1329–1337. ↵Kharchenko PV, Xi R, Park PJ. 2011. Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet 43: 1167...
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Research: Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila
- Masafumi Nozawa,
- Yohei Minakuchi,
- Kazuhiro Satomura,
- Shu Kondo,
- Atsushi Toyoda,
- and Koichiro Tamura
Genome Res. November 2021 31: 2069-2079; Published in Advance October 21, 2021, doi:10.1101/gr.275503.121
...Corresponding author: manozawa@tmu.ac.jpAbstractDosage compensation (DC) on the X Chromosome counteracts the deleterious effects of gene loss on the Y Chromosome. However, DC is not efficient if the X Chromosome also degenerates. This indeed occurs in Drosophila miranda, in which both the neo-Y and the neo...
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METHODS: Optical Mapping of BAC Clones from the Human Y Chromosome DAZ Locus
- Joseph Giacalone,
- Stephanie Delobette,
- Veronica Gibaja,
- Lei Ni,
- Yiannis Skiadas,
- Rong Qi,
- Joanne Edington,
- Zhongwu Lai,
- Damara Gebauer,
- Hongjuan Zhao,
- Thomas Anantharaman,
- Bhubaneswar Mishra,
- Laura G. Brown,
- Richa Saxena,
- David C. Page,
- and David C. Schwartz
Genome Res. September 1, 2000 10: 1421-1429; doi:10.1101/gr.112100
..., and evolutionary conservation of DAZLA , a candidate male sterility gene. Genomics 41 : 227 – 235 . ↵ Shan Z. , Hirschmann P. , Seebacher T. , Edelman A. , Jauch A. , Morell J. , Urbitsch P. , Vogt P.H. ( 1996 ) A SPGY copy homologous to the mouse gene Dazla and the Drosophila gene boule is autosomal and expressed...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...class of SVs, first identified by Sturtevant in 1917 (Sturtevant 1917), that play a key dual role in primate evolution and predisposition to disease. Chromosome inversions are the most common rearrangements differentiating humans and the great ape species at the karyotypic level (Yunis et al. 1980...

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